EP1680504B1 - Optimierte mikroorganismenstämme für nadph verbrauchende biosynthesewege - Google Patents

Optimierte mikroorganismenstämme für nadph verbrauchende biosynthesewege Download PDF

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EP1680504B1
EP1680504B1 EP04805397A EP04805397A EP1680504B1 EP 1680504 B1 EP1680504 B1 EP 1680504B1 EP 04805397 A EP04805397 A EP 04805397A EP 04805397 A EP04805397 A EP 04805397A EP 1680504 B1 EP1680504 B1 EP 1680504B1
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strain
dehydrogenase
hydroxybutyrate
gene
nadp
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EP1680504A1 (de
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Gwénaëlle BESTEL-CORRE
Cédric BOISART
Michel Chateau
Benjamin Gonzalez
Philippe Soucaille
Rainer Figge
Olivier Zink
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Metabolic Explorer SA
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    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/0004—Oxidoreductases (1.)
    • C12N9/0012—Oxidoreductases (1.) acting on nitrogen containing compounds as donors (1.4, 1.5, 1.6, 1.7)
    • C12N9/0036—Oxidoreductases (1.) acting on nitrogen containing compounds as donors (1.4, 1.5, 1.6, 1.7) acting on NADH or NADPH (1.6)
    • C—CHEMISTRY; METALLURGY
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    • C12N1/00—Microorganisms, e.g. protozoa; Compositions thereof; Processes of propagating, maintaining or preserving microorganisms or compositions thereof; Processes of preparing or isolating a composition containing a microorganism; Culture media therefor
    • C12N1/20—Bacteria; Culture media therefor
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/90—Isomerases (5.)
    • C12N9/92—Glucose isomerase (5.3.1.5; 5.3.1.9; 5.3.1.18)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12P—FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
    • C12P13/00—Preparation of nitrogen-containing organic compounds
    • C12P13/005—Amino acids other than alpha- or beta amino acids, e.g. gamma amino acids
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12P—FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
    • C12P13/00—Preparation of nitrogen-containing organic compounds
    • C12P13/04—Alpha- or beta- amino acids
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12P—FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
    • C12P33/00—Preparation of steroids
    • C12P33/12—Acting on D ring
    • C12P33/16—Acting at 17 position
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12P—FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
    • C12P7/00—Preparation of oxygen-containing organic compounds
    • C12P7/02—Preparation of oxygen-containing organic compounds containing a hydroxy group
    • C12P7/04—Preparation of oxygen-containing organic compounds containing a hydroxy group acyclic
    • C12P7/18—Preparation of oxygen-containing organic compounds containing a hydroxy group acyclic polyhydric

Definitions

  • NADP nicotinamide adenine dinucleotide phosphate
  • the present invention relates to microorganism strains optimized for the biotransformation production of molecules having NADPH-consuming biosynthetic pathways.
  • the strains according to the invention can be used in biotransformation processes consuming NADPH.
  • the strains defined according to the invention may be prokaryotic or eukaryotic.
  • said prokaryotic strain is an Escherichia coli strain .
  • said eukaryotic strain is a strain of Saccharomyces, in particular S. cerevisiae.
  • the present invention also relates to a process for preparing molecules by biotransformation comprising culturing in a suitable medium of an optimized strain according to the invention, said optimized strain also comprising the genetic elements necessary for the preparation of said molecule.
  • Biotransformation processes have been developed to allow the production of molecules in large quantities at low costs, while also allowing the valorization of different industrial by-products or agriculture.
  • the improvement of a biotransformation process can relate to various factors such as temperature, oxygenation, the composition of the medium, the recovery process, etc. It is also possible to modify the microorganism so that the production of the molecule of interest and / or its excretion is increased.
  • optimization of the biosynthetic pathway will be attempted, for example by modifying the regulation of the genes or by modifying the genes in order to modify the characteristics of the enzymes involved, or by optimizing the regeneration of the cofactors .
  • NADPH plays an important part, especially for the production of amino acids (eg arginine, proline, isoleucine, methionine, lysine), vitamins (eg panthotenate, phylloquinone, tocopherol), aromatic molecules (eg WO401564 ), polyols ( eg xylitol), polyamines ( eg spermidine). hydroxyesters (eg ethyl-4-chloro-3-hydroxybutyrate) or other high value-added molecules.
  • amino acids eg arginine, proline, isoleucine, methionine, lysine
  • vitamins eg panthotenate, phylloquinone, tocopherol
  • aromatic molecules eg WO401564
  • polyols eg xylitol
  • polyamines eg spermidine
  • hydroxyesters eg ethyl-4-chloro-3-hydroxybuty
  • the present invention thus relates to a strain of microorganisms optimized for the production of molecules having NADPH-consuming biosynthetic pathways as defined in claim 1.
  • the inventors opted for the production of modified microorganisms to obtain different ratios NADPH / NADP + , said modified microorganisms are then used to achieve consuming biotransformations of NADPH.
  • strain of microorganisms is meant according to the invention a set of microorganisms of the same species comprising at least one microorganism of said species.
  • the characteristics described for the strain apply to each of the microorganisms of said strain.
  • the characteristics described for one of the microorganisms of the strain will apply to all of said microorganisms component.
  • bacteria and yeasts filamentous fungi and in particular bacteria and yeasts of the following species: Aspergillus sp., Bacillus sp., Brevibacterium sp., Clostridium sp., Corynebacterium sp. , Escherichia sp., Gluconobacter sp., Penicillium sp., Pichia sp., Pseudomonas sp., Rhodococcus sp., Saccharomyces sp., Streptomyces sp., Xanthomonas sp., Candida sp.
  • the principle of optimizing the NADPH / NADP + ratio consists in limiting the enzymatic activities involved in the oxidation of NADPH, and in promoting the enzymatic activities allowing the reduction of NADP + .
  • the enzymatic activities involved in the oxidation of NADPH are limited by decreasing, and more particularly by inactivating, such activities, especially the quinone oxidoreductase type activities and / or soluble transhydrogenase.
  • the enzymatic activities promoting the reduction of NADP + are promoted by imposing the carbon flux via the phosphate pentose ring and / or by modifying the cofactor specificity of at least one enzyme so that it uses NADP preferentially with NADP. , his usual cofactor.
  • the optimized strains according to the invention are obtained by molecular biology. Those skilled in the art know the protocols for modifying the genetic character of microorganisms. The transformation techniques are documented and are within the reach of those skilled in the art ( Sambrook et al., 1989 Molecular cloning: a laboratory manual. 2nd Ed. Cold Spring Harbor Lab., Cold Spring Harbor, New York .).
  • the methods making it possible to limit an enzymatic activity consist in modifying the gene allowing its expression by an appropriate means, for example by providing one or more mutations (s) in the coding part of the gene concerned, or by modifying the promoter region, in particular in the replacing with a sequence to reduce the expression of the gene.
  • the methods for inactivating an enzymatic activity consist in inactivating the expression product of the gene concerned by an appropriate means, or in inhibiting the expression of the gene concerned, or in deleting at least part of the gene concerned, so as to that its expression does not take place (for example, deletion of part or all of the promoter region necessary for its expression), or the expression product has lost its function (for example deletion in the coding part of the gene concerned).
  • the deletion of a gene comprises the deletion of the essential of said gene, and optionally its replacement by a selection marker gene making it possible to facilitate the identification, isolation and purification of optimized strains according to the invention. 'invention.
  • the inactivation of a gene in E. coli is preferentially done by homologous recombination ( Datsenko, KA; Wanner, BL (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl. Acad. Sci. USA 97: 6640-6645 ).
  • the principle of a protocol is briefly recalled: a linear fragment, obtained in vitro, comprising the two regions flanking the gene, and at least one selection gene between these two regions (generally a gene for resistance to an antibiotic), said linear fragment thus having an inactivated gene.
  • the cells having undergone a recombination event and having integrated the fragment introduced by spreading on a selective medium are selected.
  • the cells which have undergone a double recombination event, in which the native gene has been replaced by the inactivated gene are then selected.
  • This protocol can be improved by using positive and negative selection systems, in order to accelerate the detection of double recombin
  • Inactivation of a gene in S. cerevisiae is also preferentially done by homologous recombination ( Baudin et al., Nucl. Acids Res. 21, 3329-3330, 1993 ; Wach et al., Yeast 10, 1793-1808, 1994 ; Brachmann et al., Yeast. 14: 115-32, 1998 ).
  • the methods making it possible to promote an enzymatic activity consist in stabilizing the expression product of the gene concerned by an appropriate means, for example by decreasing its sensitivity to allosteric effectors, or by increasing the expression of said gene in such a way as to increase the quantity enzyme.
  • Overexpression of a gene may be effected by changing the promoter of this gene in situ by a strong or inducible promoter.
  • a replicative plasmid in which the gene which one wishes to overexpress is under the control of the appropriate promoter is introduced into the cell.
  • the promoters P lac- o, P trc- o, p tac- o three strong bacterial promoters for which the lac operator (lac O ) has been deleted to return them constitutive.
  • lac O lac O
  • Saccharomyces cerevisiae it is possible , for example, to use the promoters P pgk, P adh 1 , P gal 1 and P gal 10 .
  • the methods making it possible to modify the cofactor specificity of an enzyme so that it uses NADP preferentially with NAD consist in modifying the sequence of the gene allowing the expression of this enzyme ( Bocanegra, JA Scrutton, NS; Perham, RN (1993) Creation of an NADP-dependent pyruvate dehydrogenase multienzyme complex by protein engineering. Biochemistry 32: 2737-2740 ).
  • the optimized strains according to the invention include the attenuation or inactivation of one or more NADPH oxidizing enzyme activity (s), and in particular, quinone oxidoreductase type and / or soluble transhydrogenase.
  • s NADPH oxidizing enzyme activity
  • NADPH oxidizing enzymes include, but are not limited to, the following activities and genes: Enzymatic activities EC number E. coli genes S. cerevisiae genes Alcohol dehydrogenase 1.1.1.2 Yahk ADH6 Aldose reductase 1.1.1.21 GRE3 Shikimate dehydrogenase 1.1.1.25 aroE ARO1 Methylglyoxal reductase 1.1.1.78 GRE2p Gamma-glutamyl phosphate reductase 1.2.1.41 proA PRO2 2,4-Dienoyl Coenzyme A Reductase 1.3.1.34 Fahd Glutamate dehydrogenase 1.4.1.4 gdhA GDH1, GDH2 Glutamate synthase 1.4.1.13 gltB, gltD GLT1 Methylenetetrahydrofolate dehydrogenase 1.5.1.5 fold ADE3, MIS1 Soluble transhydrogenase 1.6.1.1 ud
  • the optimized strains according to the invention ie increased NADP + reduction capacity also include modifications to favor one or more activity (s). enzymatic (s) reducing NADP + , and in particular, modifications making it possible to impose carbon flux via the pentose phosphate cycle, and / or modifications relating to the cofactor specificity of at least one enzyme, such so that it uses NADP preferentially with NAD, its usual cofactor.
  • the enzymatic activities that can be modified in the optimized strains according to the invention are defined mainly by the use of the name of the protein or the gene in E. coli or S. cerevisiae. However, this use has a more general meaning according to the invention and encompasses the corresponding enzymatic activities in other microorganisms. Indeed, by using the sequences of the proteins and genes of E. coli or S. cerevisiae, the skilled person is capable of determining the proteins and the genes equivalent in other microorganisms than E. coli or S cerevisiae.
  • the means for identifying the homologous sequences and their homology percentages are well known to those skilled in the art, including in particular the BLAST program which can be used from the site http: //www.ncbi.nlm.nih. gov / BLAST / with default settings on this site.
  • the sequences obtained can then be exploited (eg aligned) using for example the CLUSTALW programs (http://www.ebi.ac.uk/clustalw/) or MULTALTN (http://prodes.toulouse.inra.fr/multalin/cgi-bin/multalin.pl), with the parameters indicated by default on these sites.
  • CD-Search- (hthp: //www.ncbi.nih.gov/Structure/cdd/wrpsb.cgi ) which makes it possible to identify domains conserved in the protein sequences of E. coli or S. cerevisiae, and to search for sequences of other microorganisms, with the same domain (s).
  • the conserved domains are listed in the conserveed domain database (CDD) database.
  • the PFAMs (Protein FAMilies database of alignments and hidden markov models; hnp: //www.sanger.ac.uk-/Software/Pfam/) represent a large collection of protein sequence alignments . Each PFAM allows to visualize multiple alignments, to see protein domains, to evaluate the distribution between organisms, to have access to other databases, to visualize known structures of proteins.
  • COGs Clusters of Orthologous Groups of Proteins, http://www.ncbi.nlm.nih.gov/COG
  • COGs Clusters of Orthologous Groups of Proteins, http://www.ncbi.nlm.nih.gov/COG
  • Each COG is defined from of at least three lineages, which makes it possible to identify old conserved domains.
  • Genoa microorganisms qor Bradyrhizobium japonicum USDA 110 qor Brucella am 1330 CC3759 Caulobacter crescentus mll0505 Mesorhizobium loti qor Mycobacterium tuberculosis H37RV qor Pseudomonas aeruginosa ZTA1 S. cerevisiae SPCC285.01c Schizosaccharomyces pombe drgA Synechocystis sp. PCC6803 Qora Staphylococcus aureus TTC0305 Thermus thermophilus H B8 qor Yersinia pestis CO92
  • the optimized strains according to the invention include the deletion of at least one gene coding for an oxidizing activity of NADPH, and in particular the deletion of a gene coding for a quinone oxidoreductase. (eg qor , ZTA1) and / or a gene encoding a soluble transhydrogenase activity (eg udhA).
  • the udhA and qor genes are both deleted.
  • the optimized strains according to the invention also comprise the deletion of one or more gene (s) encoding the activities Phosphoglucose Isomerase (eg pgi, PG11) and / or Phosphofructokinase (eg pfkA , PFK1).
  • Phosphoglucose Isomerase eg pgi, PG11
  • Phosphofructokinase eg pfkA , PFK1
  • the optimized strains according to the invention also comprise the modification of one or more gene (s) coding for the activities Dihydrolipoamide dehydrogenase (eg lpd, LPD1) and / or Glyceraldehyde 3- phosphate dehydrogenase (eg gapA, TDH1), the modification of modifying the preference of the enzyme in favor of NADP instead of NADP, its usual cofactor.
  • Dihydrolipoamide dehydrogenase eg lpd, LPD1
  • Glyceraldehyde 3- phosphate dehydrogenase eg gapA, TDH1
  • strains according to the invention having the deletion of the genes encoding the phosphoglucose isomerase and / or phosphofructokinase activities are more particularly suitable for the biotransformation processes.
  • Glucose 6-phosphate dehydrogenase eg zwf , ZWF1
  • 6- Phosphogluconolactonase eg SOL1
  • 6-Phosphogluconate dehydrogenase eg gnd, GND1
  • Isocitrate dehydrogenase eg icd, IDP1
  • Membrane Transhydrogenase eg pntA
  • / or deleting at least one gene coding for an activity enzymatic among 6-Phosphogluconate dehydratase (eg edd), Malate synthase eg aceB, DAL7
  • Isocitrate lyase eg aceA, ICL1
  • the subject of the present invention is also a microorganism optimized for the production of NADPH as defined above and hereinafter, which also comprises one or more genes coding for enzymatic activities involved in the biotransformation of a molecule of interest. , as well as one or more selection marker genes.
  • genes may be native to the strain optimized according to the invention or introduced into the strain optimized according to the invention by transformation with an appropriate vector, either by integration into the genome of the microorganism or by a replicative vector, said appropriate vector carrying one or more genes coding for said enzymes involved in the biotransformation of said molecule of interest and / or said selection markers.
  • genes comprise a nucleic acid sequence coding for an enzyme involved in the biotransformation of the molecule of interest and / or for a selection marker, the coding sequence being fused to efficient promoter sequences in the prokaryotic and / or eukaryotic cell. chosen for the biotransformation.
  • the vector (or plasmid) may be a shuttle vector between E. coli and another microorganism.
  • the choice of the strain optimized for the NADPH / NADP + ratio will be determined according to the type of biotransformation (fermentation or bioconversion), the total NADPH demand for the bioconversion pathway considered, the nature of the source (s) (s) ) carbon (s), biomass flow demand; ...
  • the deletion of the genes coding for the activities Phosphoglucose isomerase and / or Phosphofructokinase should be essential when it is not possible to control the distribution of the carbon flux between glycolysis and the pentose phosphate pathway.
  • the deletion of the genes coding for phosphoglucose isomerase will preferably be retained for the fermentations or when the demand for NADPH requires, at a minimum, a reduction flux of 2 moles of NADP + per mole of glucose imported.
  • the deletion of the genes coding for phosphofructokinase will preferably be chosen for bioconversions or when the demand for NADPH requires, at a minimum, a reduction flux of 3-4 moles of NADP + per mole of glucose imported.
  • the present invention also relates to a process for the preparation of the optimized strains according to the invention as defined above and below, in which one deletes a gene taken from those coding for the activities Quinone oxidoreductase and soluble transhydrogenase, and where appropriate.
  • the process for preparing the strains according to the invention also comprises the transformation of the optimized strains with at least one appropriate vector comprising one or more gene (s) coding for one or more enzymes. involved in the biotransformation of a molecule of interest, as well as one or more gene (s) marker (s) selection.
  • Another aspect of the invention relates to the use of these optimized strains according to the invention for NADPH-dependent biotransformations thus allowing an improvement of the biotransformation yield compared to a non-optimized strain for NADPH.
  • biotransformations will be carried out using strains defined according to the invention in which will be expressed genes coding for enzymatic activities catalyzing NADPH-dependent reactions.
  • enzymes for example, and without this list being limited to enzymes EC 1.1.1.10 L-xylulose reductase, EC 1.1.1.21 methylglyoxal reductase, EC 1.1.1.51 3 (or 17) ⁇ -hydroxysteroid dehydrogenase, EC 1.1.1.54 allyl-alcohol dehydrogenase, EC 1.1.1.80 isopropanol dehydrogenase, EC 1.1 .1.134 dTDP-6-deoxy-L-talose 4-dehydrogenase, EC 1.1.1.149 20 ⁇ -hydroxysteroid dehydrogenase, EC 1.1.1.151 21-hydroxysteroid dehydrogenase, EC 1.1.1.189 prostaglandin-E 2 9-reductase
  • the molecule of interest is chosen from amino acids, vitamins, sterols, flavonoids, fatty acids, organic acids, polyols and hydroxyesters.
  • amino acids or their precursors include in particular lysine, methionine, threonine, proline, glutamic acid, homoserine, isoleucine, valine.
  • vitamins or their precursors include pantoate, transneurosporene, phylloquinone, tocopherols.
  • sterols include squalene, cholesterol, testosterone, progesterone, cortisone.
  • flavonoids mention will be made of frambinone and vestitone.
  • organic acids mention will be made of coumaric acid or 3-hydroxypropionic acid.
  • the method also includes adding the substrate to be "converted" in the appropriate culture medium.
  • the culture medium mentioned in step b) of the process according to the invention defined above comprises at least one assimilable carbohydrate chosen from various assimilable sugars, such as glucose, galactose, sucrose, lactose, or molasses, or by-products of these sugars.
  • a particularly preferred single source of carbon is glucose.
  • Another preferred simple carbon source is sucrose.
  • the culture medium may also contain one or more substances (eg amino acids, vitamins, mineral salts, etc.) that promote the growth of the microorganism and / or the production of the molecule of interest.
  • the mineral culture medium for E. coli can thus be of identical or similar composition to an M9 medium ( Anderson, 1946, Proc. Natl. Acad. Sci.
  • the microorganisms are fermented at a temperature of between 20 ° C. and 55 ° C., preferably between 25 ° C. and 40 ° C., more particularly about 30 ° C. for S. cerevisiae and about 37 ° C. for E coli.
  • Predictive modeling is carried out using the MetOpt®-Coli algorithm, a stoichiometric model developed by METabolic EXplorer, which makes it possible to define 1) the maximum production yield of ethyl-3-hydroxybutyrate from ethylacetoacetate; 2) the best distribution of flux from glucose to ensure the growth and redox equilibrium requirements necessary for the development of the cell and reaching the maximum bioconversion yield.
  • the parameters imposed on the model include 1) a glucose import flux at 3 mmol.g -1 .h -1 , 2) a variable growth rate of 0, 0.15 and 0.25 h -1 , 3) a flow of membrane transhydrogenase ( pnt AB) variable and less than or equal to 1 mmol.g -1 .h -1 .
  • the flux limit value of membrane transhydrogenase is determined from the literature (Hanson 1979, Anderlund et al., 1999, Emmerling et al. 4) the maintenance flow was limited between 5 and 22 mmol.g -1 .h -1 .
  • Predictive modeling is performed using the MetOpt®-Scere algorithm, a stoichiometric model developed by the company, which defines 1) the maximum production yield of ethyl-3-hydroxybutyrate from ethylacetoacetate 2) the best flow distribution from glucose to ensure the growth and redox equilibrium requirements necessary for the development of the cell and the achievement of the maximum bioconversion yield.
  • the parameters imposed on the model include 1) a glucose import flux at 3 mmol.g -1 .h -1 , 2) a variable growth rate of 0, 0.15 and 0.25 h -1 , 3) a flow of maintenance less than or equal to 22 mmol.g -1 .h -1 ; 4) the reactions of aldehyde dehydrogenases (ALD2, ALD3, ALD6) are irreversible and imposed in the direction acetate + NAD (P) H ⁇ acetaldehyde + NAD (P); 5) the yeast does not have activities equivalent to udh A or pnt A, B.
  • ALD2, ALD3, ALD6 aldehyde dehydrogenases
  • the model takes into account mitochondrial and peroxisomal compartmentalization.
  • the model suggests the deletion of a gene coding for an oxidizing enzyme NADPH and in particular the gene ZTA1.
  • the strain S. cerevisiae [AZTA1] will not allow to obtain a yield equivalent to the theoretical optimum yield, because it will be difficult to maintain the adequate distribution of carbon flow between the pentose phosphate pathway and that of glycolysis , this distribution being variable with the rate of growth.
  • it will therefore be preferable to use S. cerevisiae strains [ ⁇ (ZTA1, PFK1, PFK2)] or [ ⁇ (ZTA1, PGI1)] the choice between these two strains being a function of the growth rate of the strain during the process. bioconversion.
  • the inactivation of the udhA gene is carried out by homologous recombination according to the technique described by Datsenko and Wanner (One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products, Proc Natl Acad Sci USA, 2000, 97: 6640-6645 ).
  • the chloramphenicol resistance cassette is then removed.
  • the plasmid pCP20 carrying the FLP recombinase acting at the FRT sites of the chloramphenicol resistance cassette is introduced into the recombinant strains by electroporation.
  • the loss of the antibiotic resistance cassette is verified by a PCR analysis with UdhAF and UdhAR oligonucleotides.
  • each gene is replaced by a different antibiotic resistance cassette (for example chloramphenicol for udhA and kanamycin for qor).
  • the strain obtained is E. coli [ ⁇ ( udh A, qor )] .
  • Plasmid pSK-PgapA is constructed by inserting the gapA promoter into the vector pBluescript-SK (pSK). For that, the gapA promoter of E. coli is amplified with Pwo polymerase from chromosomal DNA.
  • the PCR product obtained is then digested with the restriction enzyme Hin d III and ligated to the Hind III restriction enzyme digested pSK vector and dephosphorylated to give the plasmid pSK-PgapA.
  • the vector pSK carries an origin of replication for E. coli and an ampicillin resistance gene.
  • the plasmid pSK-PgapA is then introduced into the strain E. coli DH5 ⁇ for verification of the construction. Sequencing the gapA promoter of the plasmid pSK-PgapA with the forward M13 universal oligonucleotide is then performed to confirm the construct.
  • Plasmid pSK-PgapA carries an origin of replication for E. coli and an ampicillin resistance gene.
  • the plasmid pSK-PgapA-GRE2p is then introduced into the strain E. coli DH5 ⁇ for verification of the construction. Sequencing of the GRE2p gene of the plasmid pSK-PgapA-GRE2p with the universal oligonucleotides M13 reverse and M13 forward is then carried out to confirm the construction.
  • the validated plasmid is then introduced into the E. coli strain [ ⁇ ( udh A, qor )] (Example 2) by electroporation.
  • E. coli [ ⁇ ( udh A, qor ) pSK-PgapA-GRE2p] is then cultured in a minimum medium containing glucose and ethylacetoacetate.
  • a strain of E. coli [pSK-PgapA-GRE2p] is cultured under the same conditions.
  • E. coli strain [ ⁇ ( udh A , qor ) pSK-PgapA-GRE2p] has an increased production yield of ethyl-3-hydroxybutyrate compared to the non-optimized strain.
  • EXAMPLE 4 Construction of E. coli strain [ ⁇ ( udh A , qor, pgi ) pSK-PgapA-GRE2p] and biotransformation of ethylacetoacetate to ethyl-3-hydroxybutvrate
  • the construction is carried out in rich medium (eg LB).
  • rich medium eg LB
  • the plasmid pSK-PgapA-GRE2p (example 3) is then introduced into the strains obtained by electroporation, and the resulting E. coli strain [ ⁇ ( udh A , qor, pgi ) pSK-PgapA-GRE2p] is selected on rich medium.
  • the strain obtained is then cultured in a minimum medium containing glucose and ethylacetoacetate.
  • a strain of E. coli [pSK-PgapA-GRE2p] is cultured under the same conditions.
  • the E. coli strain [ ⁇ ( udh A , qor, pgi ) pSK-PgapA-GRE2p] has an increased production yield of ethyl-3-hydroxybutyrate compared to the non-optimized strain.
  • EXAMPLE 5 Construction of E. coli strain [ ⁇ ( udh A , qor, pgi, edd ) pSK-PgapA-GRE2p] and biotransformation of ethylacetoacetate to ethyl-3-hydroxybutyrate
  • the construction is carried out in rich medium (eg LB).
  • rich medium eg LB
  • the plasmid pSK-PgapA-GRE2p (example 3) is then introduced into the strain obtained E. coli [ ⁇ (udh A, qor, pgi, edd )] by electroporation, and the resulting strain E. coli [ ⁇ ( udhA, qor , pgi, edd ) pSK-PgapA-GRE2p] is selected on rich medium.
  • E. coli A ( udhA, qor, pgi, edd ) pSK-PgapA-GRE2p] is then cultured in a minimum medium containing glucose and ethylacetoacetate.
  • An E. coli strain [pSK-PgapA-GRE2p] is cultured under the same conditions.
  • strain E. coli [ ⁇ ( udhA, qor, pgi, edd ) pSK-PgapA-GRE2p] has an increased production yield of ethyl-3-hydroxybutyrate compared to the non-optimized strain.
  • Example 6 Construction of E. coli strain [ ⁇ ( udhA, gor, pfkA, pfkB ) pSK-PgapA-GRE2p] and biotransformation of ethylacetoacetate to ethyl-3-hydroxybutyrate
  • the construction is carried out in rich medium (eg LB).
  • rich medium eg LB
  • the plasmid pSK-PgapA-GRE2p (Example 3) is then introduced into the strain obtained E. coli [ ⁇ ( udh A , qor, pfkA, pfkB )) by electroporation, and the resulting strain E. coli [ ⁇ ( udh A , qor, pfkA, pfkB ) pSK-PgapA-GRE2p] is selected on rich medium.
  • E. coli [ ⁇ ( udh A , qor, pfkA, pfkB) pSK-PgapA-GRE2p] is then cultured in a minimum medium containing glucose and ethylacetoacetate.
  • An E. coli strain [pSK-PgapA-GRE2p] is cultured under the same conditions.
  • the strain E. coli [ ⁇ ( udh A, qor, pfkA, pfkB ) pSK-PgapA-GRE2p] has an increased production yield of ethyl-3-hydroxybutyrate compared to the non-optimized strain.
  • Example 7 Construction of E. coli strain [ ⁇ ( udhA, qor, pgi, lpd) p lpd *, pSK-PgapA-GRE2p] and biotransformation of ethylacetoacetate to ethyl-3-hydroxybutyrate
  • the lpd gene coding for the NAD-dependent dihydrolipoamide dehydrogenase, which is involved in the multienzyme complex pyruvate dehydrogenase, is deleted using the technique described in Example 2 except that the initial strain is the E. coli strain [ ⁇ ( udh A , qor, pgi )] described in Example 4 instead of being a wild strain.
  • the construction and selection of the modified strain is carried out in a rich medium ( eg LB).
  • the strain obtained is E. coli [ ⁇ ( udh A , qor, pgi, lpd )] .
  • the plasmid p -lpd * is constructed which allows the overexpression of a NADP-dependent dihydrolipoamide dehydrogenase.
  • a NADP-dependent dihydrolipoamide dehydrogenase There are different possibilities for modifying the cofactor specificity of an enzyme.
  • Bocanegra et al. (1993) disclose a method for creating a NADP-dependent dihydrolipoamide dehydrogenase.
  • Plasmids p-lpd * and pSK-PgapA-GRE2p are then introduced by electroporation into the E. coli strain [ ⁇ ( udhA, qor, pgi, lpd )] , alternatively, one can choose to clone lpd * on pSK-PgapA- GRE2p; the plasmid pSK-PgapA-GRE2p-lpd * would then be obtained which would be introduced by electroporation into the E. coli strain [ ⁇ ( udhA, qor, pgi, lpd )] .
  • the construction and selection of the modified strain is carried out in a rich medium ( eg LB).
  • E. coli [ ⁇ ( udhA, qor, pgi, lpd ) pSK-PgapA-GRE2p, p-lpd *)] is then cultured in a minimum medium containing glucose and ethylacetoacetate.
  • An E. coli strain [pSK-PgapA-GRE2p] is cultured under the same conditions.
  • strain E. coli [ ⁇ ( udhA, qor, pgi, lpd ) pSK-PgapA-GRE2p, p -lpd * )] has an increased production yield of ethyl-3-hydroxybutyrate compared to the strain not optimized.
  • Plasmid pYGK is constructed by insertion of the Ppgk promoter, the multicloning site and the cyc1 terminator of the pYPG2 vector into the vector pBluescript-SK (pSK). For this, the P pkk promoter, the multicloning site and the cyc1 terminator are amplified with the Pfu Turbo polymerase from the pYPG2 vector.
  • the PCR product obtained is then digested with the restriction enzymes SacII - NotI and ligated to the pSK vector digested with the tapaI - SmaI restriction enzymes , ligated and then digested with the NotI - SacII restriction enzymes and dephosphorylated to give the plasmid pYGK.
  • the plasmid pYGK is then introduced into the strain E. coli DH5 ⁇ for verification of the construction. Sequencing of the P pk promoter, the multicloning site and the cyc1 terminator of the plasmid pYGK with the universal M13 reverse and M13 forward oligonucleotides is then carried out to confirm the construction.
  • the PCR product obtained is then digested with the ApaI-SmaI restriction enzymes and ligated to the ApaI- SmaI restriction enzyme digested pYGK vector and dephosphorylated to give the plasmid pYGK-GRE2p.
  • the plasmid pYGK-GRE2p is then introduced into the strain E. coli DH5 ⁇ for verification of the construction. Sequencing of the GRE2p gene of the plasmid pYGK-GRE2p with the universal oligonucleotides M13 reverse and M13 forward is then carried out to confirm the construction.
  • the plasmid pRSGK-GRE2p is finally obtained by digesting plasmids pYGK-GRE2p and pRS426 with the restriction enzymes NotI-SacII and then ligation.
  • Example 9 Construction of the S. cerevisiae strain [ ⁇ (ZTA1) pRSGK-GRE2p] and biotransformation of ethylacetoacetate to ethyl-3-hydroxybutyrate
  • Inactivation of the ZTA1 gene is achieved by inserting a marker (antibiotic resistance, auxotrophy) while deleting most of the gene of interest.
  • a marker antibiotic resistance, auxotrophy
  • the technique used is described by Brachmann et al. (Designer deletion strains derived from Saccharomyces cerevisiae S288C: a useful set of strains and plasmids for PCR-mediated gene disruption and other applications, Yeast, 1998, 14: 115-32 ).
  • We can also use the technique described by Wach et al. New heterologous modules for classical or PCR-based gene disruptions in Saccharomyces cerevisiae, Yeast, 1994, 10: 1793-1808 ).
  • a strain ⁇ (ZTA1) available, e.g. EUROSCARF strain Y33183 (genotype: BY4743; Mat a / ⁇ , His 3D1 / his 3D1; leu2D0 / leu2D0; lys 2D0 / LYS2 ; MET 15 / met15 D0; ura3 D0 / ura3 D0; YBR046c :: kan MX4 / YBR046c :: kan MX4). It is then possible after sporulation to recover a homozygous strain S. cerevisiae [ ⁇ (ZTA1) pRSGK-GRE2p].
  • the S. cerevisiae [ ⁇ (ZTA1) pRSGK-GRE2p] strain is then cultured in a minimum medium containing glucose and ethylacetoacetate.
  • the S. cerevisiae control strain [pRSGK-GRE2p] is cultivated under the same conditions.
  • strain S. cerevisiae [ ⁇ (ZTA1) pRSGK-GRE2p] has an increased production yield of ethyl-3-hydroxybutyrate compared to the non-optimized strain.
  • Example 10 Construction of the strain S. cerevisiae [ ⁇ (ZTA1, PGI1) pRSGK-GRE2p] and biotransformation of ethylacetoacetate to ethyl-3-hydroxybutyrate
  • strain A for example the strain EUROSCARF Y23336 (Mat ⁇ / a; his 3D1 / his3D1; leu2D0 / leu2D0; lys2D0 / LYS2; MET15 / met15D0; ura3D0 / ura3D0; YBR196c: : kanMX4 / YBR196c).
  • the strain is then transformed with the plasmid pRSGK-GRE2p (Example 8) and then the deletion of the ZTA1 gene is carried out using the technique described in Example 9.
  • the strain obtained S. cerevisiae [ ⁇ (ZTA1, PGI1) pRSGK-GRE2p] is then cultured in a minimum medium containing glucose and ethylacetoacetate.
  • the control strain S. cerevisiae [pRSGK-GRE2p] is grown under the same conditions.
  • strain S. cerevisiae [ ⁇ (ZTA1, PGI1) pRSGK-GRE2p] has an increased production yield of ethyl-3-hydroxybutyrate compared to the non-optimized strain.
  • Example 11 Construction of the strain S. cerevisiae [ ⁇ (ZTA1, PFK1, PFK2) pRSGK-GRE2p] and biotransformation of ethylacetoacetate to ethyl-3-hydroxybutyrate
  • the strain is then transformed with the plasmid pRSGK-GRE2p (Example 8).
  • the strain obtained S. cerevisiae [ ⁇ (ZTA1, PFK1, PFK2) pRSGK-GRE2p] is then cultured in a minimum medium containing glucose and ethylacetoacetate.
  • the control strain S. cerevisiae [pRSGK-GRE2p] is grown under the same conditions.
  • strain S. cerevisiae [ ⁇ (ZTA1, PFK1, PFK2) pRSGK-GRE2p] has an increased production yield of ethyl-3-hydroxybutyrate compared to the non-optimized strain.
  • mol EHB / mol Glucose S. cerevisiae [pRSGK-GRE2p] In progress S. cerevisiae [ ⁇ (ZTA1, PFK1, PFK2) pRSGK-GRE2p] In progress
  • Examples 1 to 11 above are particular applications of the patent and do not limit the use thereof. Those skilled in the art will readily adapt these examples for the biotransformation of molecules having a NADPH-dependent synthesis.
  • the MetOpt ® algorithm and the optimization strategy of a NADPH-dependent bioconversion process via optimization of the NADPH / NADP + ratio is validated; it also allows us to claim an expanded application to all dependent NADPH biotransformations, which can be modeled and predicted by MetOpt ® or one of its derivatives, using E. coli , S. cerevisiae or any other microorganism.
  • Example 12 shows that the MetOpt® models developed by the company are applicable to bioconversions and should more generally apply to biotransformations such as fermentations.
  • the MetOpt®-Coli model is applied to the production of cysteine or 3-hydroxypropionate by fermentation of glucose in optimized E. coli strains according to the invention.
  • the parameters used are the same as in example 1, namely: 1) a glucose import flux at 3 mmol.g -1 .h -1 , 2) a variable growth rate of 0, 0.15 and 0.25 h -1 , 3) a flow of membrane transhydrogenase ( pnt AB) variable and less than or equal to 1 mmol.g -1 .h -1 .
  • the flux limit value of membrane transhydrogenase is determined from the literature (Hanson 1979, Anderlund et al. , 1999, Emmerling et al. 4) the maintenance flow was limited between 5 and 22 mmol.g -1 .h -1 .
  • 3-hydroxypropionate is carried out in E. coli strains containing the genes coding for the enzymes of the 3-hydroxypropionate synthesis pathway, for example Chloroflexus aurantiacus malonyl-coA reductase ( Hügler et al., Journal of Bacteriology, 2002, 184: 2404-2410 ).
  • Example 14 Calculation of the theoretical optimal yields in the context of fermentation processes in S. cenevisiae ; application to the production of hydrocortisone
  • Example 12 shows that the MetOpt® models developed by the company are applicable to bioconversions and should more generally apply to biotransformations such as fermentations.
  • the MetOpt®-Scere model is applied to the production of hydrocortisone by fermentation of glucose in S strains. cerevisiae optimized according to the invention.
  • the parameters used are the same as in example 1, namely: 1) a glucose import flux at 3 mmol.g -1 .h -1 , 2) a variable growth rate of 0, 0.15 and 0.25 h -1 , 3) a maintenance flow less than or equal to 22 mmol.g -1 .h -1 ; 4) the reactions of the aldehyde dehydrogenases (ALD2, ALD3, ALD6) are irreversible and imposed in the direction acetate + NAD (P) H ⁇ acetaldehyde + NAD (P); 5) the yeast does not have activities equivalent to udh A or pnt A, B.
  • the model takes into account mitochondrial and peroxisomal compartmentalization.
  • Hydrocortisone production is carried out in S. cerevisiae strains containing the genes encoding the enzymes of the hydrocortisone synthesis pathway ( Szczebara et al., 2003, Nature Biotechnology, 21: 143-149 ).

Claims (10)

  1. Mikroorganismusstamm, dadurch gekennzeichnet, dass er die Einschränkung einer oder mehrerer NADPH oxidierender Aktivität(en) durch die Deletion eines oder mehrerer Gene umfasst, welche(s) eine Chinon-Oxidoreduktase und/oder eine lösliche Transhydrogenase codiert/codieren, und dass er auch Modifikationen umfasst, die es erlauben, eine oder mehrere enzymatische NADP+ reduzierende Aktivität(en) durch die Deletion eines oder mehrerer Gene, welche(s) eine Phosphoglucose-Isomerase und/oder eine Phosphofructokinase codiert/codieren, zu begünstigen.
  2. Mikroorganismusstamm gemäß Anspruch 1, dadurch gekennzeichnet, dass er auch die Modifikation eines oder mehrerer Gene umfasst, welche(s) eine Dihydrolipoamid-Dehydrogenase und/oder eine Glyceraldehyd-3-Phosphat-Dehydrogenase codiert/codieren, damit es/sie vorzugsweise das NADP verwendet/verwenden.
  3. Mikroorganismusstamm gemäß einem der Ansprüche 1 oder 2, dadurch gekennzeichnet, dass er auch die Überexpression eines oder mehrerer Gene umfasst, welche(s) eine Glukose-6-Phosophat-Dehydrogenase, eine 6-Phosphogluconolactonase, eine 6-Phosphogluconat-Deyhdrogenase, eine Isocitrat-Dehydrogenase oder eine membranständige Transhydrogenase codiert/codieren.
  4. Mikroorganismusstamm gemäß einem der Ansprüche 1 bis 3, dadurch gekennzeichnet, dass er auch die Deletion eines oder mehrerer Gene umfasst, welche(s) eine 6-Phosphogluconat-Dehydratase, eine Malatsynthase, eine Isocitratlyase oder eine Isocitrat-Dehydrogenase-Kinase/Phosphatase codiert/codieren.
  5. Mikroorganismusstamm gemäß einem der Ansprüche 1 bis 4, dadurch gekennzeichnet, dass er ein oder mehrere Gene, endogen oder exogen, umfasst, welche(s) Enzyme codiert/codieren, die an der Biotransformation eines Moleküls von Interesse beteiligt sind.
  6. Mikroorganismusstamm gemäß einem der Ansprüche 1 bis 5, dadurch gekennzeichnet, dass er ein oder mehrere Selektionsmarkergen(e) umfasst.
  7. Mikroorganismusstamm gemäß einem der Ansprüche 1 bis 6, dadurch gekennzeichnet, dass er aus den folgenden Arten ausgewählt ist: Aspergillus sp., Bacillus sp., Brevibacterium sp., Clostridium sp., Corynebacterium sp., Escherichia sp., Gluconobacter sp., Penicillium sp., Pichia sp., Pseudomonas sp., Rhodococcus sp., Saccharomyces sp., Streptomyces sp., Xanthomonas sp. und Candida sp.
  8. Verfahren zur Herstellung der optimierten Stämme gemäß einem der Ansprüche 1 bis 7, dadurch gekennzeichnet, dass ein oder mehrere Gen(e) deletiert wird/werden, welche(s) eine Chinon-Oxidoreduktase und/oder eine lösliche Transhydrogenase codiert/codieren, und dass ein oder mehrere Gen(e) deletiert wird/werden, welche(s) eine Phosphoglucose-Isomerase, eine Phosphofructokinase, eine 6-Phosphogluconat-Dehydratase, eine Malatsynthase, eine Isocitratlyase oder eine Isocitrat-Dehydrogenase-Kinase/Phosphatase codiert/codieren, und/oder ein oder mehrere Gen(e) modifiziert wird/werden, welche(s) eine Dihydrolipoamid-Dehydrogenase und/oder eine Glyceraldehyd-3-Phosphat-Dehydrogenase codiert/codieren, damit es/sie vorzugsweise das NADP verwendet/verwenden, wobei diese Deletionen und Modifikationen mit einem geeigneten Mittel durchgeführt werden, und/oder dass ein oder mehrere Gen(e) überexprimiert wird/werden, welche(s) eine Glukose-6-Phosophat-Dehydrogenase, eine 6-Phosphogluconolactonase, eine 6-Phosphogluconat-Dehydrogenase, eine Isocitrat-Dehydrogenase oder eine membranständige Transhydrogenase codiert/codieren, entweder durch Transformation des Stammes mit einem geeigneten Vektor, der ein oder mehrere Gen(e) umfasst, die ein oder mehrere Enzym(e), die an der Biotransformation eine Moleküls von Interesse beteiligt sind, und/oder ein oder mehrere Selektionsmarkergen(e) codiert/codieren, oder durch Modifikation der Stärke des oder der endogenen Promotors/Promotoren, welche(r) das oder die zu überexprimierende(n) Gen(e) kontrolliert/kontrollieren.
  9. Verfahren zur Herstellung eines Moleküls von Interesse, bei dem zumindest eine der Reaktionen des Biosynthesewegs NADPH-abhängig ist, dadurch gekennzeichnet, dass es die folgenden Schritte umfasst:
    a) Züchten von optimierten Mikroorganismusstämmen gemäß einem der Ansprüche 1 bis 7 in einem Kulturmedium, das geeignet ist, ihr Wachstum zu begünstigen und das die Substanzen umfasst, die für die Durchführung der Biotransformation durch Fermentation oder Biotransformation notwendig sind, mit Ausnahme von NADPH, und
    b) Extraktion des Moleküls von Interesse aus dem Medium und gegebenenfalls Aufreinigung.
  10. Verfahren gemäß Anspruch 9, dadurch gekennzeichnet, dass das Molekül von Interesse ausgewählt ist aus Aminosäuren, Vitaminen, Sterolen, Flavonoiden, Fettsäuren, organischen Säuren, Polyolen und Hydroxyestern.
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CN1875096A (zh) 2006-12-06
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BRPI0415774B1 (pt) 2019-12-31
BRPI0415774A (pt) 2006-12-26
CN103952335B (zh) 2016-08-31
FR2862068B1 (fr) 2007-10-12
CN103952335A (zh) 2014-07-30
JP2007510411A (ja) 2007-04-26
FR2862068A1 (fr) 2005-05-13
AU2004289859A1 (en) 2005-05-26
AU2004289859B2 (en) 2009-03-26
ZA200603590B (en) 2007-07-25
WO2005047498A1 (fr) 2005-05-26
US8088620B2 (en) 2012-01-03
JP5553956B2 (ja) 2014-07-23
ES2371648T3 (es) 2012-01-05
US20070087403A1 (en) 2007-04-19
KR101149566B1 (ko) 2012-07-05
IL174890A0 (en) 2006-08-20
EP1680504A1 (de) 2006-07-19
RU2006119625A (ru) 2007-12-27
KR20060132577A (ko) 2006-12-21

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